Journal Club on Biophysics and Statistical Physics at KIAS
The purpose of this journal club is to bring together researchers from physics, computational sciences and mathematics in KIAS to learn about what is life. :) Each meeting is usually 1 hr long (including questions). Everything is in English. Discussions are kept at a very elementary level; no previous knowledge about biology or statistical physics is assumed. All are welcome!
To discussion leaders: Please put the information and supplementary materials (links to published papers, slides, etc.) of your presentations below. font size: 14px
Jan 2014: "A New Physics Theory of Life" featuring Jeremy England (MIT)'s recent work of relating entropy production to origin and evolution of life. (see link here)
Title: How D-form DNAs have Two conformational states: the effects of local denaturation
Speaker: O-chul Lee (Pohang University of Science and Technology)
Abstract: Sharp bending of DNA over the nanometer length scale is ubiquitous in many cellular processes, such as packing on nucleosome, transcription control step and viral genome packing. It was possible to make a short DNA with D-geometry, (a hybrid of a circular single strand and a complementary linear strand). The FRET measurement has suggested the extension of the ds part transforms from a single state into two states, depending upon the circular length. To understand how D-form DNA has two conformational states, we study base-pair opening along the ds part as a function of ds extension, by simulating the breathing DNA model. We find that the two states are due to emergence of local denaturation in the middle and ends of the ds, namely a bubble and two forks, respectively. We also estimate the size of the bubble and forks and critical tension for the bifurcation, combining the FRET and simulation data with analytical results for the free energy of the D-DNA. It demonstrates that, in short DNA subject to a high tension, a uniformly bent state with transient bubbles and a kinked state with a permanent bubble coexist.
References:
Past Meetings:
June 19, 2015
Topic: Active matter: an overview.
Discussion leader: Wanming Qi (Physics)
Description: The study of active matter deals with the non-equilibrium many-body systems composed of self-drive ("active") particles, each is capable of converting stored or ambient free energy into systematic motion. Examples include flocks of birds, schools of fish, cytoskeleton in living cells, and the collective motions of cells in wound healing, embryonic development and cancer metastasis. It may be seen as a physicists' attempt to incorporate living matter into the condensed matter physics that is traditionally concerned with nonliving matter. I will talk about examples of active matter, and my personal impression about what people are studying in this field and why/how their results are interesting to both physicists and biologists. Then I will talk about experiments, Vicsek model, quantification of collective orders and symmetries, and the Boltzmann-Ginzburg-Landau approach for directly coarse-graining the microscopic model.
References (You may read them later if you find the talk interesting):
Description: Based on previous papers, we will study the general expressions of reaction rate, diffusion coefficient, and heat in unicyclic reaction network.
Paper to discuss:
B. Derrida, Velocity and Diffusion Constant of a Periodic One-Dimensional Hopping Model, J. Stat. Phys, 1983.
Z. Koza, General technique of calculating drift velocity and diffusion coefficient in arbitrary periodic system, J. Phys. A, 1999
H. Qian and D. A. Beard, Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium, Biophysical Chemistry, 2005.
Description: Physical, mathematical description of Brownian motion. Following topics will be covered: (1) Statistical properties of a sum of a large number. (2) Physical discussion of thermal random force. (3) Brownian motion.
Description: Essential statistical tools for the study of Langevin equation. First we will introduce the definitions of random variable and stochastic process. Gaussian random variables and Gaussian stochastic process will be introduced as an example. Then statistical properties of a sum of a large number will be investigated. Finally, a brief physical discussion of thermal random force (in Langevin equation) will be present.
Description: When held in temporal isolation, organisms from cyanobacteria to humans exhibit behavioral and physiological rhythms that persist with a period of about 24 hours. This is the so-called circadian clock. Although the circadian clock in the brain can be related to synchronization of firing neurons, the circadian clock is a more generic feature. This experimental paper shows that the circadian clock even exists in human red blood cells where there is no gene transcription.
Description: Derivation of Kramers rate theory. First, we will derive "Fokker-Planck equation" from Master equation and introduce "First-passage time" concept. After then Kramers rate theory will be introduced based on two theoretical tools above.
Paper to discuss:
Robert Zwanzig, Nonequilibrium Statistical Mechanics, Oxford, ch.4.2.
Description: "Expectation-Maximization algorithm" and its connection to "K-means clustering algorithm" (Wonseok) "Clustering method by Modularity optimization" (Jenny)
Description: Ergodicity breaking in bio-molecular system
How to analyse the system with broken ergodicity?
What is the structural origin of heterogeneity?
Paper discussed: same as the Jan 29 meeting.
Nov 2014
Topic: The energy-speed-accuracy trade-off in sensory adaptation
Discussion leader: Wanming Qi (Physics)
Description: About using the ideas of non-equilibrium statistical mechanics (e.g. Langevin equations, Master equations, entropy production rate, probability density current in the phase space and the breakdown of detailed balance) to understand how life adapts to different environments and why this must be operated at non-equilibrium by consuming energy.
Journal Club on Biophysics and Statistical Physics at KIAS
The purpose of this journal club is to bring together researchers from physics, computational sciences and mathematics in KIAS to learn about what is life. :)
Each meeting is usually 1 hr long (including questions). Everything is in English. Discussions are kept at a very elementary level; no previous knowledge about biology or statistical physics is assumed. All are welcome!
To discussion leaders:
Please put the information and supplementary materials (links to published papers, slides, etc.) of your presentations below.
font size: 14px
Contact person: Wanming Qi (wanming@kias.re.kr)
Interesting News:
Coming Meeting:
July 16, 2015 (Thursday), RM 7323, 11 AM -- 12 PMPast Meetings:
June 19, 2015
June 12, 2015
Apr 16, 2015
Apr 2, 2015
Mar 26, 2015
Mar 11, 2015
- Topic: Kramers Rate Theory
- Discussion leader: Wonseok Hwang (Computational Sciences)
- Description: Derivation of Kramers rate theory. First, we will derive "Fokker-Planck equation" from Master equation and introduce "First-passage time" concept. After then Kramers rate theory will be introduced based on two theoretical tools above.
- Paper to discuss:
- Robert Zwanzig, Nonequilibrium Statistical Mechanics, Oxford, ch.4.2.
Feb 26, 2015Jan 29, 2015
Jan 15, 2015
Nov 2014
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